It is often difficult to detect by eye the correct orientation of the amino-carbonylo group of GLN and ASNs. However, we can use (properly refined) temperature factors to detect outliers. We take the Z value as half the difference between the B-factor of the NE2 and OE1 divided by the standard deviation of the B-factors of the rest of the residue. An analysis of GLNs and ASNs of high resolutions structures indicates that a Z value of greater than 2.25 indicates a potential (if not probable) flip. A “Fix” button is provided in the resultant dialog make this easy to do.
This analysis was added after discussions with Atsushi Nakagawa and so is called “Nakagawa's Bees”.
The analysis does not check residues with multiple conformations.